Munoz replaced Jeff Smisek, who resigned last month in the wake of some questionable dealings with the Port Authority of New York & New Jersey.

United started running twice-weekly direct flights from Newark to Columbia, South Carolina -- not far from a vacation home of former Port Authority chairman David Samson -- in 2012. Those flights ended days after Samson stepped down in March 2014.

The route was reportedly dubbed "the chairman's flight" and was thought to be United's way of currying favor with the Port Authority.

But the Port Authority scandal was only one problem for Smisek and United.

The airline is still grappling with integration issues related to its merger with Continental five years ago.

United has ranked near the bottom of several recent customer satisfaction surveys. It also suffered an embarrassing technical glitch this summer that grounded its flights.

United also benefited from the drop in oil prices. Jet fuel expenses were $1.2 billion lower in the quarter, compared to last year.

But the dramatic plunge in crude prices is no longer universally good news for United. The company cited "travel reductions from corporate customers in the energy sector" as one reason why sales were soft.

United's stock is down more than 15% this year and has lagged rivals such as Delta(DAL), Southwest(LUV) and JetBlue(JBLU). Shares have fallen more than 3% since United said Munoz was in the hospital.

With that in mind, the decision to name Hart as the acting CEO disappointed one Wall Street analyst.

"Mr. Hart has limited experience in finance, operations or customer service, the areas that UAL is most in need of improving. We would have preferred an interim leader with more experience in these areas," said S&P Capital IQ analyst Jim Corridore in a report Tuesday.

But Hunter Keay with Wolfe Research took the opposite view.

"We've spent a bit of time with Mr. Hart and found him to be engaging, thoughtful, and possessive of leadership qualities," Keay wrote.

United executives did tout some positive signs for the company in a conference call with analysts.

COO Greg Hart, (no relation to acting CEO Brett) said that United has canceled 30,000 fewer flights so far this year than last year. He added that the company was doing a better job of managing customers' bags.

And Vice chairman Jim Compton said United's operations in China appear to be stabilizing after the huge stock market drop there this summer. Compton said bookings in China briefly dropped but have since "rebounded nicely."

Still, Compton noted that the strong dollar will continue to weigh on United's results.

Compton also said fares are expected to keep coming down as the airlines engage in a new round of price wars. That may be good news for travelers, but not for investors.